performGSVA {TNBC.CMS} | R Documentation |
Performs GSVA on gene sets. Also draws a heatmap representing GSVA scores.
performGSVA(expr, pred, gene.set = NULL, gsva.kcdf = "Gaussian")
expr |
A |
pred |
A vector of predicted consensus molecular subtypes. |
gene.set |
Gene sets provided as a list. If NULL, the hallmark pathway gene sets are used. |
gsva.kcdf |
Kernel to be used in the estimation of
the cumulative distribution function. By default,
this is set to |
This is a wrapper function of the gsva
function in the GSVA
package to compute GSVA
enrichment scores per sample and produce a heatmap
comparing them across consensus molecular subtypes.
A matrix of GSVA enrichment scores.
Liberzon, A. et al. (2015). The molecular signatures database hallmark gene set collection. Cell systems, 1, 417-425.
# Load gene expression profiles of TNBC samples data(GSE25055) # Predict consensus molecular subtypes of TNBC samples prediction <- predictCMS(expr = GSE25055) # Perform GSVA on the hallmark pathway gene sets resultGSVA <- performGSVA(expr = GSE25055, pred = prediction)